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Of course a possible out-of-universe explanation is that this inconsistency was just ignored by the filmmakers (since Independence Day is not that famous for its realistic plot).
But one could also come up with some possible in-universe explanations for this:
I didn't get the impression that the ship was really different from all those others, maybe they ...

I think that the movie was expressly designed to be entertaining and break records set by Jurassic Park a couple of years earlier. You might also remember the impressive marketing campaign and hype that preceded the release of the film. Considering that the target audience was everybody, things had to be dumbed down to be accessible to everybody.
In 1996, ...

Another explaination would be that space travel would have to be at light speed or greater to make it even feasible to get anywhere in a reasonable amount of time. This is where the theory of Relativity comes into play. When traveling at light speed or above, time speeds up for non-moving objects and stays the same for those traveling at those speeds and ...

Advanced civilizations (space-faring) probably wouldn't feel compelled to re-design things every 5 years, (especially if their technological progression had slowed).
The aliens in Independence Day would be even less likely to do this since their whole reason for moving from planet to planet is a lack of resources, one of those mother-ships would require a ...

I believe that it was a reference to the movie Close Encounters of the Third Kind. In that film (the scene is on YouTube) humans use a board with flashing lights (similar to the lights on the helicopters) and music to communicate with Aliens.